We have been working on several proteomics bioinformatics tools: a project to develop an open-source proteomics expression data mining tool set (Open2Dprot) for n-dimensional protein data from various sources (2D PAGE gels, 2D LC-MS, protein arrays, etc); an improved method for visually comparing 2D gel protein samples (Flicker program) and making putative spot identifications with enhancements for characterizing nanoparticles; we recently started investigating subtle properties of 2D DIGE images (CmpDIGE program) that may help us characterize these changes, and then model and identify post-translational protein modifications of relatively small size. Open2Dprot - the open 2D proteomics expression n-dimensional data analysis project Open2Dprot is a fully open-source community proteomics project and Web site for developing tools for analyzing protein expression data from a variety of protein separation methods. Data is analyzed through an analysis pipeline that includes: accession of sample data, spot detection in samples (using image segmentation, peak clustering or other methods), registration between samples where required, spot pairing with respect to a reference sample where required, assembly of paired spot data into a composite spot database stored in a relational database, and data mining tools on subsets using both Java and R language analyses. All data files are now fully XML compatible. We have completed the initial design of the Open2Dprot pipeline data analyzer and pipeline process scheduler and have implemented a major portion of the code using dynamic methods. Data sources will include: 2D-PAGE (polyacrylamide gel electrophoresis), 2D LC-MS, protein arrays, etc. Because different separation sources require different analysis methods, the pipeline is designed so that particular steps in the pipeline can be assigned dynamically depending on the data source type. We are working with international groups developing proteomics bioinformatics database schema standards for experiment information and protein expression for these types of sample separations (MIAPE/GelML XML standards). Our goal is to work towards developing tools compatible with these developing proteomics database standards so data and analysis software could be exchanged. As an open-source tool set, it will be able to incorporate new academic (and other) advances in quantitative and qualitative protein expression analysis - including interaction with various Internet proteomic databases and system biology databases. A Web site has been set up at http://open2dprot.sourceforge.net/ that goes into more detail. As parts of the pipeline software become usable, they are made available on the Web site (see Subprojects) on the web site. These programs are written in Java and run on most computers.Flicker interactive comparison of biological samples across the Internet Flicker, http://open2dprot.sourceforge.net/Flicker, is a stand-alone software program to facilitate the interactive comparison of biological samples across the Internet. It is a major update of the previous subproject, the Flicker applet program Lemkin PF, et. al. (1999) Mol Biotechnology 12(2): 159-172. The new program is described Lemkin PF, et. al. (2005)(12Mb PDF) "Comparing 2-D Electrophoretic Gels Across Internet Databases". In The Proteomics Handbook, JM Walker (Ed), Humana Press Inc, Totowa, NJ, pp 279-305. Scientists around the world often work on similar data so the need to share results and compare data arises periodically. Flicker is a Java computer-implementation of a flicker-comparison method for comparing 2D gel image data of two similar samples created in different laboratories to help putatively identify protein spots in user's 2D gels.